miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
2511	3'	-55.8	NC_001454.1	+	16756	0.66	0.567908
	Target:  5'- gCUCCGCgGCAcgGCUcGCGGccguuuaUGGGCa -3' miRNA:   3'- gGAGGUGgCGUcaCGAuUGCC-------ACCUG- -5'
2511	3'	-55.8	NC_001454.1	+	14457	0.66	0.524837
	Target:  5'- aUUCCACCcccacuacaggGUAGuUGCUGACuugcGUGGACg -3' miRNA:   3'- gGAGGUGG-----------CGUC-ACGAUUGc---CACCUG- -5'
2511	3'	-55.8	NC_001454.1	+	16051	0.67	0.482015
	Target:  5'- uCgUCCACCGUua-GCacuGCGGUGGAg -3' miRNA:   3'- -GgAGGUGGCGucaCGau-UGCCACCUg -5'
2511	3'	-55.8	NC_001454.1	+	8894	0.68	0.421184
	Target:  5'- uCCUCCACaGCGGgacccucgggGCUGAcCGGcgcugGGACg -3' miRNA:   3'- -GGAGGUGgCGUCa---------CGAUU-GCCa----CCUG- -5'
2511	3'	-55.8	NC_001454.1	+	7770	0.69	0.365219
	Target:  5'- uUCUgCACCuGCAcgcucuUGCUGugGGUGGAUg -3' miRNA:   3'- -GGAgGUGG-CGUc-----ACGAUugCCACCUG- -5'
2511	3'	-55.8	NC_001454.1	+	20381	0.77	0.107366
	Target:  5'- gCCUCgaugaCGCCGCGGUGCggcUGGUGGAUg -3' miRNA:   3'- -GGAG-----GUGGCGUCACGauuGCCACCUG- -5'
2511	3'	-55.8	NC_001454.1	+	16113	1.12	0.000297
	Target:  5'- gCCUCCACCGCAGUGCUAACGGUGGACg -3' miRNA:   3'- -GGAGGUGGCGUCACGAUUGCCACCUG- -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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